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Make build green

Right now, for both gn2 and gn3, we have broken builds(red) for both gn3 and gn2.

Note: Pjotr made the build work again. Pushed to guix-bioinformatics.

Tasks

  • assigned: bonfacekilz, efraim
  • type: failure
  • status: complete, closed
  • keywords: build

Notes

At the moment, we are getting the following build failures in gn2,

Compiling '/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/wqflask/wgcna/wgcna_analysis.py'...
Compiling '/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/wsgi.py'...
error: in phase 'install': uncaught exception:
%exception #<&invoke-error program: "python" arguments: ("-m" "compileall" "--invalidation-mode=unchecked-hash" "/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9") exit-status: 1 term-signal: #f stop-signal: #f> 
phase `install' failed after 0.9 seconds
command "python" "-m" "compileall" "--invalidation-mode=unchecked-hash" "/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9" failed with status 1
note: keeping build directory `/tmp/guix-build-genenetwork2-3.11-guix-fe345c9.drv-0'
builder for `/gnu/store/l5hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv' failed with exit code 1
build of /gnu/store/l5hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv failed
View build log at '/var/log/guix/drvs/l5/hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv.bz2'.
guix build: error: build of `/gnu/store/l5hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv' failed

Some missing bits from the build log:

Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/redis_tools.py'...
Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/startup_config.py'...
Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/svg.py'...
***   File "/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/svg.py", line 113
    True = 1
        ^
        SyntaxError: cannot assign to True

Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/temp_data.py'...
Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/tools.py'...

This starts happening (not yet comfirmed) when python is bumped up from 3.8 to 3.9

In addition, there are some dependencies of genenetwork2 which FTBFS, due to incorrect versions of inputs.

 starting phase `sanity-check'¬
 validating 'pingouin' /gnu/store/dpy5ln4zjgv53l8jpm1qalwn45cagxfm-python-pingouin-0.5.0/lib/python3.9/site-packages¬
 ...checking requirements: ERROR: pingouin==0.5.0 (statsmodels 0.11.1 (/gnu/store/ab8k9bwmaml2bplq4bd9xkg08z7bn8fr-python-statsmodels-0.11.1/lib/python3.9/site-packages), Requirement.parse('statsmodels>=0.12.0'), {'pingouin'})¬
 error: in phase 'sanity-check': uncaught exception:¬
 %exception #<&invoke-error program: "python" arguments: ("/gnu/store/nwwr89v2vyg1hs48i49m083vhczsgh3m-sanity-check.py" "/gnu/store/dpy5ln4zjgv53l8jpm1qalwn45cagxfm-python-pingouin-0.5.0/lib/python3.9/site-packages") exit-status: 1 term-signal: #f stop-signal: #f>▸¬
 phase `sanity-check' failed after 0.1 seconds¬

This was fixed by reverting the update to python-pingouin, dropping it back to 0.3.12.


(made with skribilo)